I'd argue that your definition of a joint mission is fairly incorrect in many real-world contexts. Many would call the Korean War a NATO joint mission but it was mostly American troops. In Iraq US and British troops weren't necessarily doing the same thing, which does not mean it's not a joint mission. Just two examples for the sake of discussion. Not saying anything about that canon-breaking line in Other M, mind you, I'm just making a point where I see an issue.
Personally I'm of the "Samus forgot" explanation, since she sort of seems to forget a couple things about being Samus. (Zing!) Seriously, though, I do lean towards the "Sakamoto screwed up/didnt care" explanation and I pay one sentence no mind. Although now that I think about it, is the translation exactly taken from Japanese, or were there changes in that monologue? Because that could possibly explain the issue.
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